makeHCdendrogram: Plot HC dendrogram

Description Usage Arguments Value

View source: R/makeHCdendrogram.R

Description

Plot HC dendrogram given a data frame.

Usage

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makeHCdendrogram(
  df,
  sample_to_color_map,
  method_distance = "euclidean",
  method_agglomeration = "complete",
  main = "hierarchical clustering dendrogram"
)

Arguments

df

A data frame on which PCA plot is based.

sample_to_color_map

A data frame mapping sample names to color. Make sure the order of row of 'sample_to_color_map' is the same as order of columns in 'df'. Make sure there is column named 'color'.

method_distance

A character of method for calculating distances between samples. Defaults to "euclidean". Can also be one of:"maximum", "manhattan", "canberra", "binary", "minkowski", "pearson", "kendall", "spearman". The last free are derived from fdistColPearson() function.

method_agglomeration

A character of sample clustering method. Defaults to "complete" (i.e. complete linkage algorithm). Can also be one of: "ward.D", "ward.D2", "single","average","mcquitty","median","centroid". See ?hclust for more info.

Value

A HC dendrogram


msxakk89/dat documentation built on Aug. 3, 2020, 6:39 p.m.